Question: miRNA pipeline guide
0
gravatar for jiovy1991
17 days ago by
jiovy19910
jiovy19910 wrote:

Hello, i'm an university student, as an end-of-course project I have to perform a pipeline for miRNA, as in the image ...., you could suggest me which tools to use and how to proceed. pipeline Thank you all

sequencing • 125 views
ADD COMMENTlink modified 17 days ago • written 17 days ago by jiovy19910
1
gravatar for giorgio.giurato
17 days ago by
giorgio.giurato10 wrote:

Hi, You can use cutadapt to remove adapter sequences and bowtie to map the reads. A good tool Is sRNAbench or SPAR

ADD COMMENTlink modified 17 days ago • written 17 days ago by giorgio.giurato10

thanks for the answer, the problem is mainly related to the computational resources we have (a machine with 16gb ram and i7-7700HQ), in fact trying to index the entire human genome (hg38) with BWA (used in a tutorial in the classroom) crashes due to lack of resources ... I'll try the tools mentioned.

ADD REPLYlink written 17 days ago by jiovy19910

Try to download the indexed genome from here http://emea.support.illumina.com/sequencing/sequencing_software/igenome.html

ADD REPLYlink written 17 days ago by giu.lat820
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